Workflow: protein_evidence_mapping.cwl
Fetched 2025-03-26 08:59:14 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| eval | Float (Optional) | Maximum e-val for stage 1 |
Maximum e-val to accept for the region_finding step (stage 1) |
| max_intron | Integer (Optional) | Maximum intron length |
Maximum intron length, passed to metaeuk |
| min_intron | Integer (Optional) | Minimum intron length |
Minimum intron length, passed to metaeuk and spaln |
| min_coverage | Float (Optional) | Minimum coverage |
Minimum proportion of a gene structure covered by exons |
| contigs_fasta | File [FASTA] | Genomic contigs (FASTA) | |
| species_table | String (Optional) | Spaln species table to use (optional) | |
| proteins_fasta | File [FASTA] | Proteins (FASTA) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| spaln |
tools/spaln.cwl
(CommandLineTool)
|
||
| metaeuk |
tools/metaeuk_easy_predict.cwl
(CommandLineTool)
|
||
| extract_region_pairs |
make_search_pair_workflow.cwl
(Workflow)
|
||
| extract_region_specs |
tools/metaeuk_to_regions.cwl
(CommandLineTool)
|
||
| process_spaln_output |
tools/process_spaln_output.cwl
(CommandLineTool)
|
||
| samtools_index_contigs |
https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/samtools/samtools_faidx.cwl
(CommandLineTool)
|
||
| samtools_index_protein |
https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/samtools/samtools_faidx.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| spaln_out | File |
Permalink:
https://w3id.org/cwl/view/git/a36f4eb493cece18c90634ee45dd2d97276fe4d3/protein_evidence_mapping.cwl
